Stack auto-removes dependency from .cabal file following 'stack build'

I want to work on a new Haskell project using the threepenny-gui package.

The first thing I did was create a stack project via $ stack new threepennydemo. From here, here, I did the following:

1. I edited the extra-deps section in my stack.yaml file from:

# extra-deps: []

to

extra-deps:
  - threepenny-gui-0.9.0.0

2. I edited the .cabal file from:

library
  exposed-modules:
      Lib
  other-modules:
      Paths_threepennydemo
  hs-source-dirs:
      src
  build-depends:
      base >=4.7 && <5
  default-language: Haskell2010

executable threepennydemo-exe
  main-is: Main.hs
  other-modules:
      Paths_threepennydemo
  hs-source-dirs:
      app
  ghc-options: -threaded -rtsopts -with-rtsopts=-N
  build-depends:
      base >=4.7 && <5
    , threepennydemo
  default-language: Haskell2010

test-suite threepennydemo-test
  type: exitcode-stdio-1.0
  main-is: Spec.hs
  other-modules:
      Paths_threepennydemo
  hs-source-dirs:
      test
  ghc-options: -threaded -rtsopts -with-rtsopts=-N
  build-depends:
      base >=4.7 && <5
    , threepennydemo
  default-language: Haskell2010

to

library
  exposed-modules:
      Lib
  other-modules:
      Paths_threepennydemo
  hs-source-dirs:
      src
  build-depends:
      base >=4.7 && <5
    , threepenny-gui >= 0.9
  default-language: Haskell2010

executable threepennydemo-exe
  main-is: Main.hs
  other-modules:
      Paths_threepennydemo
  hs-source-dirs:
      app
  ghc-options: -threaded -rtsopts -with-rtsopts=-N
  build-depends:
      base >=4.7 && <5
    , threepennydemo
    , threepenny-gui >= 0.9
  default-language: Haskell2010

test-suite threepennydemo-test
  type: exitcode-stdio-1.0
  main-is: Spec.hs
  other-modules:
      Paths_threepennydemo
  hs-source-dirs:
      test
  ghc-options: -threaded -rtsopts -with-rtsopts=-N
  build-depends:
      base >=4.7 && <5
    , threepennydemo
    , threepenny-gui >= 0.9
  default-language: Haskell2010

3. I edited the stock /app/Main.hs from:

module Main where

import Lib

main :: IO ()
main = someFunc

to

import Graphics.UI.Threepenny
main :: IO ()
main = do
 startGUI defaultConfig showMessage
showMessage :: Window -> UI ()
showMessage window = do
 getBody window #+ [string "Hello, world!"]
 return ()

4. I enter the command $ stack build.

From here, I notice two things. The first is that I receive the following error:

Building all executables for `threepennydemo' once. After a successful build of all of them, only specified executables will be rebuilt.
threepennydemo> configure (lib + exe)
Configuring threepennydemo-0.1.0.0...
threepennydemo> build (lib + exe)
Preprocessing library for threepennydemo-0.1.0.0..
Building library for threepennydemo-0.1.0.0..
Preprocessing executable 'threepennydemo-exe' for threepennydemo-0.1.0.0..
Building executable 'threepennydemo-exe' for threepennydemo-0.1.0.0..
[1 of 2] Compiling Main

/Users/my_username/threepennydemo/app/Main.hs:1:1: error:
    Could not load module ‘Graphics.UI.Threepenny’
    It is a member of the hidden package ‘threepenny-gui-0.9.0.0’.
    Perhaps you need to add ‘threepenny-gui’ to the build-depends in your .cabal file.
    Use -v (or `:set -v` in ghci) to see a list of the files searched for.
  |
1 | import Graphics.UI.Threepenny
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


--  While building package threepennydemo-0.1.0.0 using:
      /Users/my_username/.stack/setup-exe-cache/x86_64-osx/Cabal-simple_mPHDZzAJ_3.0.1.0_ghc-8.8.4 --builddir=.stack-work/dist/x86_64-osx/Cabal-3.0.1.0 build lib:threepennydemo exe:threepennydemo-exe --ghc-options " -fdiagnostics-color=always"
    Process exited with code: ExitFailure 1

The second is that my .cabal file, edited as mentioned in 2., has automatically removed the edits I made to the file.

What am I missing in order to be able to use a third party library when setting up a new stack project?

My difficulty as the result of some confusion between stack.yaml and package.yaml. The latter being what generates the threepennydemo.cabal file. Hence, dependencies must also be specified to a package.yaml file. Adding this dependency to the package.yaml allowed $ stack build to complete without issue.